Update Wed Nov 4 13:24:03 2015

Sanity check

Correlation with protein-coding gene RPKM

Differentially marked genes

MZ twins

## [1] "No enrichment for DM_H3K27me3_Brain_Subject2.pc"

## [1] "No enrichment for DM_H3K27me3_Cortex_Subject2.pc"

  • Brain01 vs Brain02: DE genes that are DM in both H3K4me3 and H3K27me3
    name description
    ARSD arylsulfatase_D_[Source:HGNC_Symbol;Acc:717]
    ADIPOR2 adiponectin_receptor_2_[Source:HGNC_Symbol;Acc:24041]
    KPNA6 karyopherin_alpha_6_(importin_alpha_7)_[Source:HGNC_Symbol;Acc:6399]
    CD38 CD38_molecule_[Source:HGNC_Symbol;Acc:1667]
    DERA deoxyribose-phosphate_aldolase_(putative)_[Source:HGNC_Symbol;Acc:24269]
    HCCS holocytochrome_c_synthase_[Source:HGNC_Symbol;Acc:4837]
    RHBDF1 rhomboid_5_homolog_1_(Drosophila)_[Source:HGNC_Symbol;Acc:20561]
    C8B complement_component_8,beta_polypeptide[Source:HGNC_Symbol;Acc:1353]
    DEF6 differentially_expressed_in_FDCP_6_homolog_(mouse)_[Source:HGNC_Symbol;Acc:2760]
    VIM vimentin_[Source:HGNC_Symbol;Acc:12692]
    TYROBP TYRO_protein_tyrosine_kinase_binding_protein_[Source:HGNC_Symbol;Acc:12449]
    DYRK4 dual-specificity_tyrosine-(Y)-phosphorylation_regulated_kinase_4_[Source:HGNC_Symbol;Acc:3095]
    BIRC3 baculoviral_IAP_repeat_containing_3_[Source:HGNC_Symbol;Acc:591]
    IL32 interleukin_32_[Source:HGNC_Symbol;Acc:16830]
    PHTF2 putative_homeodomain_transcription_factor_2_[Source:HGNC_Symbol;Acc:13411]
    SEC62 SEC62_homolog_(S.cerevisiae)[Source:HGNC_Symbol;Acc:11846]
    GPR124 G_protein-coupled_receptor_124_[Source:HGNC_Symbol;Acc:17849]
    HHATL hedgehog_acyltransferase-like_[Source:HGNC_Symbol;Acc:13242]
    COX15 COX15_homolog,cytochrome_c_oxidase_assembly_protein(yeast)_[Source:HGNC_Symbol;Acc:2263]
    SCYL3 SCY1-like_3_(S.cerevisiae)[Source:HGNC_Symbol;Acc:19285]
    MNAT1 menage_a_trois_homolog_1,cyclin_H_assembly_factor(Xenopus_laevis)_[Source:HGNC_Symbol;Acc:7181]
    SYN1 synapsin_I_[Source:HGNC_Symbol;Acc:11494]
    C1orf201 chromosome_1_open_reading_frame_201_[Source:HGNC_Symbol;Acc:28070]
    JHDM1D jumonji_C_domain_containing_histone_demethylase_1_homolog_D_(S.cerevisiae)[Source:HGNC_Symbol;Acc:22224]
    LGALS14 lectin,_galactoside-binding,_soluble,14[Source:HGNC_Symbol;Acc:30054]
    SERPINB1 serpin_peptidase_inhibitor,clade_B(ovalbumin),member_1[Source:HGNC_Symbol;Acc:3311]
    XYLT2 xylosyltransferase_II_[Source:HGNC_Symbol;Acc:15517]
    SLC38A5 solute_carrier_family_38,member_5[Source:HGNC_Symbol;Acc:18070]
    TEAD3 TEA_domain_family_member_3_[Source:HGNC_Symbol;Acc:11716]
    SNAPC1 small_nuclear_RNA_activating_complex,_polypeptide_1,43kDa[Source:HGNC_Symbol;Acc:11134]
    BRCA1 breast_cancer_1,early_onset[Source:HGNC_Symbol;Acc:1100]
    MTMR11 myotubularin_related_protein_11_[Source:HGNC_Symbol;Acc:24307]
    IDS iduronate_2-sulfatase_[Source:HGNC_Symbol;Acc:5389]
    UBR7 ubiquitin_protein_ligase_E3_component_n-recognin_7_(putative)_[Source:HGNC_Symbol;Acc:20344]
    PHF20 PHD_finger_protein_20_[Source:HGNC_Symbol;Acc:16098]
    C12orf4 chromosome_12_open_reading_frame_4_[Source:HGNC_Symbol;Acc:1184]
    VCL vinculin_[Source:HGNC_Symbol;Acc:12665]
    ARNTL2 aryl_hydrocarbon_receptor_nuclear_translocator-like_2_[Source:HGNC_Symbol;Acc:18984]
    RABEP1 rabaptin,RAB_GTPase_binding_effector_protein_1[Source:HGNC_Symbol;Acc:17677]
  • Brain01 vs Brain02: DE genes that are DM in both DMR and H3K27me3
name description
AGK acylglycerol_kinase_[Source:HGNC_Symbol;Acc:21869]
RAD52 RAD52_homolog_(S.cerevisiae)[Source:HGNC_Symbol;Acc:9824]
PGM3 phosphoglucomutase_3_[Source:HGNC_Symbol;Acc:8907]
CCL18 chemokine_(C-C_motif)ligand_18(pulmonary_and_activation-regulated)_[Source:HGNC_Symbol;Acc:10616]
TBXA2R thromboxane_A2_receptor_[Source:HGNC_Symbol;Acc:11608]
AGPS alkylglycerone_phosphate_synthase_[Source:HGNC_Symbol;Acc:327]
TG thyroglobulin_[Source:HGNC_Symbol;Acc:11764]
XK X-linked_Kx_blood_group_(McLeod_syndrome)_[Source:HGNC_Symbol;Acc:12811]
  • Cortex01 vs Cortex02: DE genes that are DM in both DMR and H3K27me3
name description
JHDM1D jumonji_C_domain_containing_histone_demethylase_1_homolog_D_(S.cerevisiae)[Source:HGNC_Symbol;Acc:22224]
SPATA20 spermatogenesis_associated_20_[Source:HGNC_Symbol;Acc:26125]
TNFRSF12A tumor_necrosis_factor_receptor_superfamily,member_12A[Source:HGNC_Symbol;Acc:18152]
ETV1 ets_variant_1_[Source:HGNC_Symbol;Acc:3490]
CCL3 chemokine_(C-C_motif)ligand_3[Source:HGNC_Symbol;Acc:10627]
ITGA2B integrin,alpha_2b(platelet_glycoprotein_IIb_of_IIb/IIIa_complex,antigen_CD41)[Source:HGNC_Symbol;Acc:6138]
CELSR3 cadherin,EGF_LAG_seven-pass_G-type_receptor_3(flamingo_homolog,Drosophila)[Source:HGNC_Symbol;Acc:3230]
IKZF2 IKAROS_family_zinc_finger_2_(Helios)_[Source:HGNC_Symbol;Acc:13177]
DERA deoxyribose-phosphate_aldolase_(putative)_[Source:HGNC_Symbol;Acc:24269]
ZNF806 zinc_finger_protein_806_[Source:HGNC_Symbol;Acc:33228]
BID BH3_interacting_domain_death_agonist_[Source:HGNC_Symbol;Acc:1050]
RAB27B RAB27B,member_RAS_oncogene_family[Source:HGNC_Symbol;Acc:9767]
PTBP1 polypyrimidine_tract_binding_protein_1_[Source:HGNC_Symbol;Acc:9583]
PLEKHO1 pleckstrin_homology_domain_containing,family_O_member_1[Source:HGNC_Symbol;Acc:24310]
ANK1 ankyrin_1,erythrocytic[Source:HGNC_Symbol;Acc:492]
RTN4R reticulon_4_receptor_[Source:HGNC_Symbol;Acc:18601]
  • GE01 vs GE02: DE genes that are DM in both DMR and H3K27me3
name description
ADIPOR2 adiponectin_receptor_2_[Source:HGNC_Symbol;Acc:24041]

NPCs

  • Cortex01 vs GE01: DE genes that are DM in both DMR and H3K7me3
name description
TCIRG1 T-cell,_immune_regulator_1,_ATPase,_H+_transporting,lysosomal_V0_subunit_A3[Source:HGNC_Symbol;Acc:11647]
AGT angiotensinogen_(serpin_peptidase_inhibitor,_clade_A,member_8)[Source:HGNC_Symbol;Acc:333]
FES feline_sarcoma_oncogene_[Source:HGNC_Symbol;Acc:3657]
ECHDC3 enoyl_CoA_hydratase_domain_containing_3_[Source:HGNC_Symbol;Acc:23489]
DOCK9 dedicator_of_cytokinesis_9_[Source:HGNC_Symbol;Acc:14132]
ELF4 E74-like_factor_4_(ets_domain_transcription_factor)_[Source:HGNC_Symbol;Acc:3319]
CTSZ cathepsin_Z_[Source:HGNC_Symbol;Acc:2547]
NEK9 NIMA_(never_in_mitosis_gene_a)-related_kinase_9[Source:HGNC_Symbol;Acc:18591]
NA Uncharacterized_protein_[Source:UniProtKB/TrEMBL;Acc:A8MV45]
KIAA1244 KIAA1244_[Source:HGNC_Symbol;Acc:21213]
TMEM132B transmembrane_protein_132B_[Source:HGNC_Symbol;Acc:29397]
ITPR3 inositol_1,4,5-trisphosphate_receptor,type_3[Source:HGNC_Symbol;Acc:6182]
THSD7A thrombospondin,_type_I,domain_containing_7A[Source:HGNC_Symbol;Acc:22207]
TSPYL5 TSPY-like_5_[Source:HGNC_Symbol;Acc:29367]
CYP27A1 cytochrome_P450,_family_27,_subfamily_A,polypeptide_1[Source:HGNC_Symbol;Acc:2605]
PYGL phosphorylase,_glycogen,liver[Source:HGNC_Symbol;Acc:9725]
LIPG lipase,endothelial[Source:HGNC_Symbol;Acc:6623]
FUT9 fucosyltransferase_9_(alpha_(1,3)fucosyltransferase)[Source:HGNC_Symbol;Acc:4020]
OTX1 orthodenticle_homeobox_1_[Source:HGNC_Symbol;Acc:8521]
TFCP2 transcription_factor_CP2_[Source:HGNC_Symbol;Acc:11748]
GSX2 GS_homeobox_2_[Source:HGNC_Symbol;Acc:24959]
COL23A1 collagen,_type_XXIII,alpha_1[Source:HGNC_Symbol;Acc:22990]
C13orf15 chromosome_13_open_reading_frame_15_[Source:HGNC_Symbol;Acc:20369]
MDK midkine_(neurite_growth-promoting_factor_2)_[Source:HGNC_Symbol;Acc:6972]
TSKU tsukushi_small_leucine_rich_proteoglycan_homolog_(Xenopus_laevis)_[Source:HGNC_Symbol;Acc:28850]
LRRC10B leucine_rich_repeat_containing_10B_[Source:HGNC_Symbol;Acc:37215]
ID2 inhibitor_of_DNA_binding_2,dominant_negative_helix-loop-helix_protein[Source:HGNC_Symbol;Acc:5361]
APCDD1 adenomatosis_polyposis_coli_down-regulated_1_[Source:HGNC_Symbol;Acc:15718]
COL9A3 collagen,_type_IX,alpha_3[Source:HGNC_Symbol;Acc:2219]
APOE apolipoprotein_E_[Source:HGNC_Symbol;Acc:613]
C10orf90 chromosome_10_open_reading_frame_90_[Source:HGNC_Symbol;Acc:26563]
PRDM1 PR_domain_containing_1,with_ZNF_domain[Source:HGNC_Symbol;Acc:9346]
LMO3 LIM_domain_only_3_(rhombotin-like_2)_[Source:HGNC_Symbol;Acc:6643]
VAX1 ventral_anterior_homeobox_1_[Source:HGNC_Symbol;Acc:12660]
FZD5 frizzled_family_receptor_5_[Source:HGNC_Symbol;Acc:4043]
CXCR7 chemokine_(C-X-C_motif)receptor_7[Source:HGNC_Symbol;Acc:23692]
FEZF1 FEZ_family_zinc_finger_1_[Source:HGNC_Symbol;Acc:22788]
CYTL1 cytokine-like_1_[Source:HGNC_Symbol;Acc:24435]
KCTD12 potassium_channel_tetramerisation_domain_containing_12_[Source:HGNC_Symbol;Acc:14678]
CHST6 carbohydrate_(N-acetylglucosamine_6-O)sulfotransferase_6[Source:HGNC_Symbol;Acc:6938]
BRSK2 BR_serine/threonine_kinase_2_[Source:HGNC_Symbol;Acc:11405]
OTX2 orthodenticle_homeobox_2_[Source:HGNC_Symbol;Acc:8522]
  • Cortex02 vs GE02: DE genes that are DM in DMR, H3K4me3, and H3K7me3
name description
PAX6 paired_box_6_[Source:HGNC_Symbol;Acc:8620]
EMX2 empty_spiracles_homeobox_2_[Source:HGNC_Symbol;Acc:3341]
TMEM132B transmembrane_protein_132B_[Source:HGNC_Symbol;Acc:29397]
TFCP2 transcription_factor_CP2_[Source:HGNC_Symbol;Acc:11748]
HOPX HOP_homeobox_[Source:HGNC_Symbol;Acc:24961]
C10orf90 chromosome_10_open_reading_frame_90_[Source:HGNC_Symbol;Acc:26563]
SFTA3 surfactant_associated_3_[Source:HGNC_Symbol;Acc:18387]
VAX1 ventral_anterior_homeobox_1_[Source:HGNC_Symbol;Acc:12660]
TBX2 T-box_2_[Source:HGNC_Symbol;Acc:11597]
SIX3 SIX_homeobox_3_[Source:HGNC_Symbol;Acc:10889]
SLIT2 slit_homolog_2_(Drosophila)_[Source:HGNC_Symbol;Acc:11086]
NKX2-1 NK2_homeobox_1_[Source:HGNC_Symbol;Acc:11825]
DLX1 distal-less_homeobox_1_[Source:HGNC_Symbol;Acc:2914]

GW

  • GE02 vs GE04: DE genes that are DM in DMR, H3K4me3, and H3K27me3
name description
HIST4H4 histone_cluster_4,H4[Source:HGNC_Symbol;Acc:20510]
OCIAD2 OCIA_domain_containing_2_[Source:HGNC_Symbol;Acc:28685]
C6orf201 chromosome_6_open_reading_frame_201_[Source:HGNC_Symbol;Acc:21620]
RHCG Rh_family,C_glycoprotein[Source:HGNC_Symbol;Acc:18140]
ISLR2 immunoglobulin_superfamily_containing_leucine-rich_repeat_2_[Source:HGNC_Symbol;Acc:29286]
EMILIN1 elastin_microfibril_interfacer_1_[Source:HGNC_Symbol;Acc:19880]
EPHA1 EPH_receptor_A1_[Source:HGNC_Symbol;Acc:3385]
CCDC8 coiled-coil_domain_containing_8_[Source:HGNC_Symbol;Acc:25367]
VAX1 ventral_anterior_homeobox_1_[Source:HGNC_Symbol;Acc:12660]
SIX3 SIX_homeobox_3_[Source:HGNC_Symbol;Acc:10889]
ARAP3 ArfGAP_with_RhoGAP_domain,ankyrin_repeat_and_PH_domain_3[Source:HGNC_Symbol;Acc:24097]
NKX2-1 NK2_homeobox_1_[Source:HGNC_Symbol;Acc:11825]
OTX2 orthodenticle_homeobox_2_[Source:HGNC_Symbol;Acc:8522]
OLIG2 oligodendrocyte_lineage_transcription_factor_2_[Source:HGNC_Symbol;Acc:9398]
EDNRB endothelin_receptor_type_B_[Source:HGNC_Symbol;Acc:3180]
ZIC5 Zic_family_member_5_[Source:HGNC_Symbol;Acc:20322]
SP8 Sp8_transcription_factor_[Source:HGNC_Symbol;Acc:19196]
FZD7 frizzled_family_receptor_7_[Source:HGNC_Symbol;Acc:4045]

Core enhancers

GWAS in core enhancers

  • 1460 enhancers overlap with GWAS, involved in 546 traits.
  • Several traits are related to brain development and function: Cortical structure, Glaucoma (exfoliation), Glioblastoma, Neuranatomic and neurocognitive phenotypes, Neuroblastoma (high-risk), Odorant perception (isobutyraldehyde), Schizophrenia (cytomegalovirus infection interaction), Alzheimer’s disease biomarkers.

Homer TFBSs

  • There are 13 TFs significantly (Benjamini q value < 0.01) enriched in core enhancers and present in > 20% of the core enhancers.
  • Ptf1a: plays an important role in cerebellar and pancreatic development.
  • Isl1: central to the development of pancreatic cell lineages and may also be required for motor neuron generation.
  • Lhx3: involved in the development of interneurons and motor neurons.
  • NF1: negative regulator of the ras signal transduction pathway, associated with neurofibromatosis type 1.
  • Sox3: function as a switch in neuronal development. Keeps neural cells undifferentiated by counteracting the activity of proneural proteins and suppresses neuronal differentiation.
  • Olig2: oligodendrocyte specific marker.

Overlapping with WGBS UMRs

  • UMRs between neurospheres (cortex vs GE) are enriched in enhancers (H3K4me1 enriched regions).
  • Between gestational weeks, GW13 UMRs are enriched in enhancers, but GW17 UMRs are not.
  • UMRs overlaped with enhancers are highly enriched for brain development terms. For comparing between neurospheres, GE enhancer UMRs in HuFNSC04 have no significant enrichment. And for comparing between gestational weeks, GW13 enhancer UMRs in Cortex also have no enriched terms.

Unique enhancers

Comparison Samples Sample1 Sample2 Sample1_unique Sample2_unique
MZ Brain01_Brain02 69300 58831 30038 18240
MZ Cortex01_Cortex02 125995 105033 35489 5466
MZ GE01_GE02 135489 102950 47186 3765
Neurospheres Cortex01_GE01 125995 135489 14961 24022
Neurospheres Cortex02_GE02 105033 102950 23099 18732
GW GE01_GE04 135489 102477 49603 6361
GW GE02_GE04 102950 102477 22826 22889

Functional enrichment of unique enhancers

  • For MZ twins, no GREAT enriched terms in cortex and GE. In mixed brain, HuFNSC02 unique enhancers show brain organ development terms, WNT pathway, and kidney-related terms.
  • For cortex and GE progenitors, both showed brain-related terms, more so in cortex.
  • For GWs, both GW13 and GW17 unique enhancers showed enrichment for brain organ development terms. GW17 also showed WNT pathway terms.

GWAS in unique enhancers

  • All sets of unique enhancers showed brain or brain disease related GWAS sites, such as Gliomas, Alzheimer’s disease, Autism, Schizophrenia or bipolar disorder, Cognitive performance, Neuroblastoma (high-risk), Normalized brain volume, Intelligence.

Homer TFBSs

Unique enhancers between GW13 and GW17

  • Intersect of unique enhancers between GE01 vs GE04 and GE02 vs GE04. There are 5840 GW13-specific enhancers, and 17909 GW17-specific enhancers.
  • There are 52 TFs significantly (Benjamini q-value < 0.01) enriched in GW13-specific enhancers, and 117 in GW17-specific enhancers. Among them, 42 TFs are in common.
  • In the common TFs, 9 are present in > 20% enhancers in either GW13 or GW17. Their percent occupancy in GW13 and GW17 specific enhancers are similar, and downstream target genes are significantly overlapped (for example, Sox3 hypergeometric test p-value = 0).
  • There are only 10 GW13-specific TFs, and they all present in < 5% of the enhancers.
  • There are 75 GW17-specific TFs, and 5 of them are present in > 20% of the enhancers, including Olig2.
  • GW17-specific enhancers overlapped with Olig2 binding sites are associated with 3 GW-specific DE genes in cortex, and 28 in GE. Both gene lists are enriched for neuron development terms.

  • Olig2 downstream DE genes in cortex (distance to TSS < 10kb)
  • EMX2: Empty Spiracles Homeobox 2. acts to generate the boundary between the roof and archipallium in the developing brain. May function in combinations with OTX1/2 to specify cell fates in the developing central nervous system.
  • RGS10: Regulator Of G-Protein Signaling 10. associated with schizophrenia.
  • LGI1: Leucine-Rich, Glioma Inactivated 1. This gene is predominantly expressed in neural tissues and its expression is reduced in low grade brain tumors and significantly reduced or absent in malignant gliomas. Mutations in this gene result in autosomal dominant lateral temporal epilepsy. May play a role in the control of neuroblastoma cell survival.

Olig2_cortex_DE

  • Olig2 downstream DE genes in GE (distance to TSS < 10kb)
  • PAX6: Paired Box 6. expressed in the developing nervous system, and in developing eyes. Mutations in this gene are known to cause ocular disorders such as aniridia and Peter’s anomaly.
  • HIVEP2: Human Immunodeficiency Virus Type I Enhancer Binding Protein 2. zinc finger-containing transcription factors. The encoded protein regulates transcription by binding to regulatory regions of various cellular and viral genes that maybe involved in growth, development and metastasis.

Olig2_GE_DE

Unique enhancers between cortex and GE

  • Intersect of unique enhancers between cortex01 vs GE01 and cortex02 vs GE02. There are 3279 cortex-specific enhancers, and 5731 GE-specific enhancers.
  • There are 42 TFs significantly (Benjamini q-value < 0.01) enriched in cortex-specific enhancers, and 78 in GE-specific enhancers. Among them, 32 TFs are in common.
  • In the common TFs, 11 are present in > 20% enhancers in either cortex or GE. Their percent occupancy in cortex and GE specific enhancers are similar, and downstream target genes are significantly overlapped (for example, Lhx3 hypergeometric test p-value = 0).
  • There are only 10 cortex-specific TFs, and they all present in < 20% of the enhancers.
  • There are 46 GW17-specific TFs, and 4 of them are present in > 20% of the enhancers, including Olig2.
  • 252 GE-specific enhancers overlapped with Olig2 binding sites are associated with NPC-specific DE genes, and the DE genes are enriched for neuron development terms.